3F3M

Six Crystal Structures of Two Phosphopantetheine Adenylyltransferases Reveal an Alternative Ligand Binding Mode and an Associated Structural Change


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of Staphylococcus aureus phosphopantetheine adenylyltransferase in complex with 3'-phosphoadenosine 5'-phosphosulfate reveals a new ligand-binding mode

Lee, H.H.Yoon, H.J.Kang, J.Y.Park, J.H.Kim, D.J.Choi, K.H.Lee, S.K.Song, J.Kim, H.J.Suh, S.W.

(2009) Acta Crystallogr.,Sect.F 65: 987-991

  • DOI: 10.1107/S1744309109036616

  • PubMed Abstract: 
  • Bacterial phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in the coenzyme A (CoA) biosynthetic pathway. It catalyzes the reversible transfer of an adenylyl group from ATP to 4'-phosphopantetheine (Ppant) to form dephospho ...

    Bacterial phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in the coenzyme A (CoA) biosynthetic pathway. It catalyzes the reversible transfer of an adenylyl group from ATP to 4'-phosphopantetheine (Ppant) to form dephospho-CoA (dPCoA) and pyrophosphate. Previous structural studies have revealed how several ligands are recognized by bacterial PPATs. ATP, ADP, Ppant and dPCoA bind to the same binding site in a highly similar manner, while CoA binds to a partially overlapping site in a different mode. To provide further structural insights into ligand binding, the crystal structure of Staphylococcus aureus PPAT was solved in a binary complex with 3'-phosphoadenosine 5'-phosphosulfate (PAPS). This study unexpectedly revealed a new mode of ligand binding to PPAT, thus providing potentially useful information for structure-based discovery of inhibitors of bacterial PPATs.


    Organizational Affiliation

    Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphopantetheine adenylyltransferase
A
168Staphylococcus aureus (strain MW2)Mutation(s): 0 
Gene Names: coaD
EC: 2.7.7.3
Find proteins for P63820 (Staphylococcus aureus (strain MW2))
Go to UniProtKB:  P63820
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PPS
Query on PPS

Download SDF File 
Download CCD File 
A
3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE
C10 H15 N5 O13 P2 S
GACDQMDRPRGCTN-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.211 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 66.774α = 90.00
b = 66.774β = 90.00
c = 124.134γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data scaling
CNSrefinement
HKL-2000data collection
CNSphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-04-25
    Type: Database references